kgd1 (SPBC3H7.03c; UniProt O74378) encodes the E1 (2-oxoglutarate dehydrogenase, thiamine diphosphate-dependent; EC 1.2.4.2) subunit of the mitochondrial 2-oxoglutarate dehydrogenase complex. With E2 (kgd2), E3 (dld1) and the adaptor kgd4, it converts 2-oxoglutarate to succinyl-CoA in the TCA cycle. Function is assigned by orthology; it is mitochondrial in a genome-wide screen.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | IBA GO_REF:0000033 | ACCEPT | Summary: E1 2-oxoglutarate dehydrogenase activity (PAINT/EC). Reason: UniProt's curated catalytic-activity line gives the E1 reaction (EC 1.2.4.2, RHEA:12188), and the protein carries the 2-oxoglutarate dehydrogenase E1 family signatures (NCBIfam TIGR00239, Pfam E1_dh). Membership of this family supports the activity; the evidence is by family and similarity to S. cerevisiae Kgd1 and other donors, not an S. pombe enzyme assay. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = file:SCHPO/kgd1/kgd1-uniprot.txt NCBIfam; TIGR00239; 2oxo_dh_E1; 1. |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | IEA GO_REF:0000120 | ACCEPT | Summary: E1 2-oxoglutarate dehydrogenase activity (PAINT/EC). Reason: The EC/Rhea mapping matches UniProt's curated catalytic-activity line (EC 1.2.4.2), and the protein carries the 2-oxoglutarate dehydrogenase E1 family signature (NCBIfam TIGR00239). Family-based, not an S. pombe enzyme assay. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = file:SCHPO/kgd1/kgd1-uniprot.txt NCBIfam; TIGR00239; 2oxo_dh_E1; 1. |
| GO:0005739 mitochondrion | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: ORFeome YFP screen: mitochondrion. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of mitochondrial location. Reason: UniProt places kgd1 in the mitochondrial matrix by similarity (ECO:0000250), and the sequence has a predicted N-terminal mitochondrial transit peptide (residues 1-39, ECO:0000255). Two independent lines agree on the organelle; the HDA ORFeome row also places it in mitochondria. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix file:SCHPO/kgd1/kgd1-uniprot.txt TRANSIT 1..39 |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Matrix location of this TCA enzyme (inference or mapping); consistent. Reason: UniProt's matrix location is by similarity (ECO:0000250) to orthologous E1o subunits; a predicted mitochondrial transit peptide (1-39) and the soluble E1 enzyme role in the matrix-resident OGDH complex agree. No S. pombe sub-mitochondrial assay is cited. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix file:SCHPO/kgd1/kgd1-uniprot.txt TRANSIT 1..39 |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference; TCA cycle step. Reason: UniProt's function statement (by similarity, ECO:0000250) says the 2-oxoglutarate dehydrogenase complex converts 2-oxoglutarate to succinyl-CoA and CO2, the TCA cycle step; kgd1 is its E1 component by family membership (TIGR00239). Ortholog/family evidence. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2) file:SCHPO/kgd1/kgd1-uniprot.txt NCBIfam; TIGR00239; 2oxo_dh_E1; 1. |
| GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: Generic InterPro-derived parent of the specific E1 activity, which is already annotated. Reason: The term is correct but general. UniProt's curated catalytic-activity line gives the specific E1 2-oxoglutarate dehydrogenase reaction (EC 1.2.4.2), and the protein carries the 2-oxoglutarate dehydrogenase E1 family signature (NCBIfam TIGR00239). The replacement GO:0004591 is already on the gene (ACCEPT). Family and ortholog evidence, not an S. pombe assay. Proposed replacements: oxoglutarate dehydrogenase (succinyl-transferring) activity Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt Reaction=N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = file:SCHPO/kgd1/kgd1-uniprot.txt NCBIfam; TIGR00239; 2oxo_dh_E1; 1. |
| GO:0030976 thiamine pyrophosphate binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Thiamine diphosphate cofactor of the E1 component; subsidiary to the dehydrogenase activity. Reason: The thiamine diphosphate cofactor and its binding residues are assigned by similarity to S. cerevisiae Kgd1 (ECO:0000250|UniProtKB:Q02218), and the protein carries the thiamine diphosphate-binding fold signature (InterPro IPR029061). Ortholog and family evidence. Non-core because cofactor binding serves the E1 activity. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937; file:SCHPO/kgd1/kgd1-uniprot.txt InterPro; IPR029061; THDP-binding. |
| GO:0042645 mitochondrial nucleoid | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Similarity transfer of mitochondrial nucleoid association from S. cerevisiae, where polypeptides of the alpha-ketoglutarate dehydrogenase complex co-purify with mtDNA nucleoids. Not shown in S. pombe. Reason: The evidence is from S. cerevisiae, where nucleoid isolation unexpectedly recovered polypeptides of the alpha-ketoglutarate dehydrogenase complex alongside mtDNA packaging proteins (Kaufman et al., as summarised in PMID:14597775). No S. pombe nucleoid study is cached. This is a moonlighting association, peripheral to the E1 activity, so it stays non-core. Supporting Evidence: PMID:14597775 It was surprising, however, to find other abundant proteins, such as Aco1p, some polypeptides of the Ξ±-ketoglutarate dehydrogenase complex, and the chaperonin Hsp60, whose functions are ostensibly unrelated to mtDNA inheritance. |
| GO:0045252 oxoglutarate dehydrogenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: E1 subunit of the 2-oxoglutarate dehydrogenase complex. Reason: UniProt's function statement (by similarity, ECO:0000250) describes the complex as containing the E1 2-oxoglutarate dehydrogenase, E2 and E3 components; kgd1 is an E1 family member (TIGR00239). Ortholog/family evidence; not shown biochemically in S. pombe. Supporting Evidence: file:SCHPO/kgd1/kgd1-uniprot.txt contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1) file:SCHPO/kgd1/kgd1-uniprot.txt NCBIfam; TIGR00239; 2oxo_dh_E1; 1. |
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